Mackenzie Weygandt Mathis

Xiaohang Yu, Ti Wang, Mackenzie Weygandt Mathis

We present PRIMA (*PRI*ors for *M*esh *A*daptation), a framework for robust 3D quadruped mesh recovery under severe species and pose imbalance. Existing animal reconstruction methods often regress toward mean shapes and poses due to limited 3D supervision and long-tailed species distributions, resulting in poor generalization to underrepresented animals and rare articulations. PRIMA addresses this challenge through three key contributions. First, we incorporate BioCLIP embeddings as biological priors to inject semantic and morphological knowledge into the reconstruction process, enabling more accurate and generalizable shape prediction across diverse quadrupeds. Second, we introduce a test-time adaptation (TTA) strategy that refines SMAL predictions using 2D reprojection constraints together with auxiliary keypoint guidance, improving pose and shape estimation while enabling the generation of high-quality pseudo-3D annotations from existing 2D datasets. Third, leveraging this TTA framework, we construct Quadruped3D, a large-scale pseudo-3D dataset that covers diverse species and pose variations to systematically improve model performance. Extensive experiments on Animal3D, CtrlAni3D, Quadruped2D, and Animal Kingdom demonstrate that PRIMA achieves state-of-the-art results, with particularly strong improvements on underrepresented species and challenging poses. Our results highlight the importance of biological priors and adaptation-driven data expansion for scalable and generalizable animal mesh recovery. Code is available at https://github.com/AdaptiveMotorControlLab/PRIMA.

Mu Zhou, Lucas Stoffl, Mackenzie Weygandt Mathis et al.

Frequent interactions between individuals are a fundamental challenge for pose estimation algorithms. Current pipelines either use an object detector together with a pose estimator (top-down approach), or localize all body parts first and then link them to predict the pose of individuals (bottom-up). Yet, when individuals closely interact, top-down methods are ill-defined due to overlapping individuals, and bottom-up methods often falsely infer connections to distant bodyparts. Thus, we propose a novel pipeline called bottom-up conditioned top-down pose estimation (BUCTD) that combines the strengths of bottom-up and top-down methods. Specifically, we propose to use a bottom-up model as the detector, which in addition to an estimated bounding box provides a pose proposal that is fed as condition to an attention-based top-down model. We demonstrate the performance and efficiency of our approach on animal and human pose estimation benchmarks. On CrowdPose and OCHuman, we outperform previous state-of-the-art models by a significant margin. We achieve 78.5 AP on CrowdPose and 48.5 AP on OCHuman, an improvement of 8.6% and 7.8% over the prior art, respectively. Furthermore, we show that our method strongly improves the performance on multi-animal benchmarks involving fish and monkeys. The code is available at https://github.com/amathislab/BUCTD

Steffen Schneider, Jin Hwa Lee, Mackenzie Weygandt Mathis

Mapping behavioral actions to neural activity is a fundamental goal of neuroscience. As our ability to record large neural and behavioral data increases, there is growing interest in modeling neural dynamics during adaptive behaviors to probe neural representations. In particular, neural latent embeddings can reveal underlying correlates of behavior, yet, we lack non-linear techniques that can explicitly and flexibly leverage joint behavior and neural data. Here, we fill this gap with a novel method, CEBRA, that jointly uses behavioral and neural data in a hypothesis- or discovery-driven manner to produce consistent, high-performance latent spaces. We validate its accuracy and demonstrate our tool's utility for both calcium and electrophysiology datasets, across sensory and motor tasks, and in simple or complex behaviors across species. It allows for single and multi-session datasets to be leveraged for hypothesis testing or can be used label-free. Lastly, we show that CEBRA can be used for the mapping of space, uncovering complex kinematic features, and rapid, high-accuracy decoding of natural movies from visual cortex.

Shaokai Ye, Anastasiia Filippova, Jessy Lauer et al.

Quantification of behavior is critical in applications ranging from neuroscience, veterinary medicine and animal conservation efforts. A common key step for behavioral analysis is first extracting relevant keypoints on animals, known as pose estimation. However, reliable inference of poses currently requires domain knowledge and manual labeling effort to build supervised models. We present a series of technical innovations that enable a new method, collectively called SuperAnimal, to develop unified foundation models that can be used on over 45 species, without additional human labels. Concretely, we introduce a method to unify the keypoint space across differently labeled datasets (via our generalized data converter) and for training these diverse datasets in a manner such that they don't catastrophically forget keypoints given the unbalanced inputs (via our keypoint gradient masking and memory replay approaches). These models show excellent performance across six pose benchmarks. Then, to ensure maximal usability for end-users, we demonstrate how to fine-tune the models on differently labeled data and provide tooling for unsupervised video adaptation to boost performance and decrease jitter across frames. If the models are fine-tuned, we show SuperAnimal models are 10-100$\times$ more data efficient than prior transfer-learning-based approaches. We illustrate the utility of our models in behavioral classification in mice and gait analysis in horses. Collectively, this presents a data-efficient solution for animal pose estimation.

Ti Wang, Xiaohang Yu, Mackenzie Weygandt Mathis

Monocular 3D pose estimation is fundamentally ill-posed due to depth ambiguity and occlusions, thereby motivating probabilistic methods that generate multiple plausible 3D pose hypotheses. In particular, diffusion-based models have recently demonstrated strong performance, but their iterative denoising process typically requires many timesteps for each prediction, making inference computationally expensive. In contrast, we leverage Flow Matching (FM) to learn a velocity field defined by an Ordinary Differential Equation (ODE), enabling efficient generation of 3D pose samples with only a few integration steps. We propose a novel generative pose estimation framework, FMPose3D, that formulates 3D pose estimation as a conditional distribution transport problem. It continuously transports samples from a standard Gaussian prior to the distribution of plausible 3D poses conditioned only on 2D inputs. Although ODE trajectories are deterministic, FMPose3D naturally generates various pose hypotheses by sampling different noise seeds. To obtain a single accurate prediction from those hypotheses, we further introduce a Reprojection-based Posterior Expectation Aggregation (RPEA) module, which approximates the Bayesian posterior expectation over 3D hypotheses. FMPose3D surpasses existing methods on the widely used human pose estimation benchmarks Human3.6M and MPI-INF-3DHP, and further achieves state-of-the-art performance on the 3D animal pose datasets Animal3D and CtrlAni3D, demonstrating strong performance across both 3D pose domains. The code is available at https://github.com/AdaptiveMotorControlLab/FMPose3D.

Steffen Schneider, Rodrigo González Laiz, Anastasiia Filippova et al.

Gradient-based attribution methods aim to explain decisions of deep learning models but so far lack identifiability guarantees. Here, we propose a method to generate attribution maps with identifiability guarantees by developing a regularized contrastive learning algorithm trained on time-series data plus a new attribution method called Inverted Neuron Gradient (collectively named xCEBRA). We show theoretically that xCEBRA has favorable properties for identifying the Jacobian matrix of the data generating process. Empirically, we demonstrate robust approximation of zero vs. non-zero entries in the ground-truth attribution map on synthetic datasets, and significant improvements across previous attribution methods based on feature ablation, Shapley values, and other gradient-based methods. Our work constitutes a first example of identifiable inference of time-series attribution maps and opens avenues to a better understanding of time-series data, such as for neural dynamics and decision-processes within neural networks.

Mackenzie Weygandt Mathis

Biological intelligence is inherently adaptive -- animals continually adjust their actions based on environmental feedback. However, creating adaptive artificial intelligence (AI) remains a major challenge. The next frontier is to go beyond traditional AI to develop "adaptive intelligence," defined here as harnessing insights from biological intelligence to build agents that can learn online, generalize, and rapidly adapt to changes in their environment. Recent advances in neuroscience offer inspiration through studies that increasingly focus on how animals naturally learn and adapt their world models. In this Perspective, I will review the behavioral and neural foundations of adaptive biological intelligence, the parallel progress in AI, and explore brain-inspired approaches for building more adaptive algorithms.